RSEM v1.1.11 is online now. A bug related to expected counts calculation
is fixed. Allow spaces for field seqname and attributes gene_id and
transcript_id in GTF files.
This version changed reference indices format used by RSEM, so please
rebuild the references by using 'rsem-prepare-reference'
You can find the source code here
http://deweylab.biostat.wisc.edu/rsem/
Best,
Bo